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sidier (version 3.0.1)

Substitution and Indel Distances to Infer Evolutionary Relationships

Description

Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework.

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Version

Install

install.packages('sidier')

Monthly Downloads

166

Version

3.0.1

License

GPL-2

Maintainer

AJ MuozPajares

Last Published

February 28th, 2015

Functions in sidier (3.0.1)

ex_Coords

example coordinates

spatial.plot

spatial plot of populations

FindHaplo

Find equal haplotypes

HapPerPop

Returns the number of haplotypes per population.

FIFTH

Indel distances following the fifth state rationale

BARRIEL

Indel distances following Barriel method

nt.gap.comb

substitution and indel distance combinations

colour.scheme

internal function for node colour scheme

mutation.network

Haplotype network depiction including mutations

simuEvolution

Simulate sequences evolution

mergeNodes

Merges nodes showing distance values equal to zero

NINA.thr

No Isolated Nodes Allowed network

Example_Spatial.plot_Alignment

example alignment #1 (fasta format)

SIC

Indel distances following the Simple Index Coding method

sidier-package

SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships

simplify.network

Network showing modules as nodes

distance.comb

Distance matrices combination

perc.thr

Percolation threshold network

double.plot

Haplotype and population networks including mutations and haplotype frequencies.

pop.dist

Distances among populations

GetHaplo

Get sequences of unique haplotypes

pie.network

Population network depiction including haplotype frequencies

mutationSummary

Summary of observed mutations

zero.thr

Zero distance networks

single.network

Plot a network given a threshold

MCIC

Modified Complex Indel Coding as distance matrix

ex_alignment1

example alignment #1

alignExample

example alignment #1 ('DNAbin' class)